Contacts of the helix formed by residues 263 - 279 (chain R) in PDB entry 2GLJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 263 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R ASN* 5.4 0.9 - - - -
108R SER* 3.6 17.8 + - - -
262R TYR* 1.3 84.6 - - - +
264R GLN* 1.3 66.5 + - - +
265R ASP* 2.6 11.1 + - - +
267R ARG* 2.9 41.0 - - - +
445R GLU* 3.3 7.1 + - - -
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Residues in contact with GLN 264 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R ASN* 5.1 3.7 + - - +
37R ASN* 4.9 10.0 + - - +
259R VAL* 2.7 34.2 - - - +
260R MET 3.9 0.3 - - - -
261R GLY* 2.9 31.8 + - - +
262R TYR 3.2 3.2 + - - +
263R GLY* 1.3 75.1 - - - +
265R ASP* 1.3 55.2 + - - +
266R ASP 2.8 11.1 + - - -
267R ARG* 4.9 0.4 - - - -
268R ILE* 3.2 43.0 + - - +
343R VAL* 3.8 0.3 - - - +
437R LEU* 3.6 10.1 - - + +
445R GLU* 2.8 31.4 + - + +
446R ILE 4.4 0.2 - - - -
447R SER* 2.8 32.6 + - - -
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Residues in contact with ASP 265 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R HIS* 3.1 6.4 + - - +
107R ASP 4.3 0.5 - - - +
108R SER* 3.5 17.4 + - - +
109R PRO* 5.1 2.2 - - + -
263R GLY 2.6 10.1 + - - +
264R GLN* 1.3 68.7 - - - +
266R ASP* 1.3 55.7 + - - +
267R ARG* 2.6 14.0 + - - +
296R GLU* 3.0 19.3 - - - +
343R VAL* 3.4 13.3 - - + +
437R LEU* 3.9 0.7 - - - -
440R MSE 3.0 24.4 - - - +
441R HIS* 3.0 9.3 + - + -
445R GLU* 3.0 21.9 + - - +
6036R MN 2.1 32.6 + - - -
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Residues in contact with ASP 266 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R ALA* 3.2 3.8 - - - +
105R HIS* 2.4 68.4 + - + +
264R GLN 2.8 5.2 + - - -
265R ASP* 1.3 72.3 + - - +
267R ARG* 1.3 48.2 + - - +
268R ILE 2.9 5.8 - - - +
269R CYS* 2.7 10.1 + - - +
270R ALA* 2.6 34.5 + - - +
341R SER 2.7 25.7 - - - +
342R ASP* 2.9 19.1 - - - +
343R VAL* 3.3 15.6 - - - +
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Residues in contact with ARG 267 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R ASN* 4.9 2.5 + - - +
36R SER* 5.6 5.2 - - - +
37R ASN* 4.6 15.0 - - + +
40R THR* 3.6 11.3 + - - -
41R GLU* 3.3 44.8 + - - +
43R GLU* 4.2 6.5 + - - +
45R VAL* 4.1 23.9 - - + +
105R HIS 4.2 3.7 + - - -
106R ILE* 2.8 29.5 + - - +
107R ASP* 4.1 1.4 - - - +
108R SER* 3.7 27.9 + - - +
110R ARG* 6.0 0.8 - - - +
262R TYR* 4.0 6.1 + - - -
263R GLY* 2.9 35.3 + - - +
264R GLN* 4.9 0.4 - - - -
265R ASP 2.6 10.6 + - - +
266R ASP* 1.3 72.9 - - - +
268R ILE* 1.3 56.5 + - - +
270R ALA* 3.7 10.2 - - + +
271R TYR* 3.1 26.2 + - - +
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Residues in contact with ILE 268 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R ASN* 4.0 22.9 - - - +
264R GLN* 3.2 45.6 + - - +
266R ASP 2.9 0.4 - - - -
267R ARG* 1.3 77.3 - - - +
269R CYS* 1.3 67.8 + - - +
271R TYR* 3.3 2.1 + - - +
272R THR* 3.1 25.2 + - + +
343R VAL* 3.6 21.3 - - + -
435R VAL* 3.9 23.6 - - + -
437R LEU* 4.7 0.9 - - + -
447R SER* 3.8 10.8 - - - +
452R ILE* 3.7 36.1 - - + -
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Residues in contact with CYS 269 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R ALA* 4.4 1.6 - - + -
266R ASP* 2.7 17.7 + - - +
268R ILE* 1.3 85.5 - - - +
270R ALA* 1.3 53.1 + - - +
271R TYR 3.0 2.5 - - - -
272R THR* 3.1 7.9 + - - -
273R SER* 2.6 42.4 + - - -
341R SER* 3.4 18.2 - - - +
342R ASP 4.0 8.1 - - - -
343R VAL* 4.1 7.9 - - - -
434R GLY* 3.4 33.7 - - - -
435R VAL* 3.7 12.1 - - - -
459R TYR* 3.7 6.2 - - - +
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Residues in contact with ALA 270 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R VAL* 5.9 2.7 - - + -
49R ILE* 4.8 2.8 - - + +
104R ALA* 3.8 12.5 - - + +
105R HIS 4.4 1.3 - - - +
106R ILE* 4.0 17.5 - - + -
266R ASP 2.6 19.6 + - - +
267R ARG* 3.7 13.0 - - + +
269R CYS* 1.3 73.2 - - - +
271R TYR* 1.3 56.7 + - - +
273R SER* 2.8 16.2 + - - -
274R PHE* 3.3 14.7 + - - +
291R LEU* 3.9 26.3 - - + +
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Residues in contact with TYR 271 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R ASP* 4.6 5.2 - - - -
32R LYS* 2.8 20.9 + - + +
33R ASN* 3.5 39.7 - - + +
36R SER* 3.8 27.8 - - - +
45R VAL* 6.5 0.2 - - + -
49R ILE* 5.4 9.4 - - + -
267R ARG 3.1 16.6 + - - +
268R ILE 3.6 4.9 - - - +
269R CYS 3.0 0.6 - - - -
270R ALA* 1.3 75.4 - - - +
272R THR* 1.3 68.6 + - + +
273R SER 3.1 1.3 - - - -
274R PHE* 2.7 38.6 + + - +
275R GLU* 2.7 52.7 + - + +
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Residues in contact with THR 272 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R ASP* 5.2 3.4 - - - +
33R ASN* 6.1 0.2 - - + -
268R ILE* 3.1 14.6 + - + +
269R CYS* 3.1 11.4 + - - -
271R TYR* 1.3 82.3 - - + +
273R SER* 1.3 63.1 + - - +
275R GLU* 4.6 2.0 - - - +
276R ALA* 2.9 32.6 + - - +
435R VAL* 5.6 0.9 - - + -
452R ILE* 3.7 40.8 - - + +
455R THR* 3.6 5.9 - - + +
456R LYS* 3.9 27.2 - - + +
459R TYR* 3.2 15.0 - - - -
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Residues in contact with SER 273 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102R LEU* 3.8 23.5 - - - +
103R GLY 5.6 0.7 - - - -
104R ALA* 4.6 4.3 - - - +
269R CYS 2.6 24.3 + - - -
270R ALA* 2.8 21.3 + - - -
272R THR* 1.3 78.4 + - - +
274R PHE* 1.3 55.9 + - - +
276R ALA* 3.8 1.3 - - - +
277R MET* 3.0 30.0 + - - +
289R THR* 4.1 6.8 + - - +
291R LEU* 4.4 7.1 - - - +
341R SER* 5.2 2.9 - - - -
459R TYR* 3.3 23.6 - - - -
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Residues in contact with PHE 274 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R ILE* 3.2 49.6 - - + -
52R ALA* 4.0 11.9 - - + -
53R GLU* 3.2 37.9 - - + -
87R MET* 3.3 21.1 - - + -
270R ALA 3.3 12.8 - - - +
271R TYR* 2.7 30.6 + + - +
273R SER* 1.3 78.9 + - - +
275R GLU* 1.3 62.7 + - + +
277R MET* 2.9 6.9 + - - +
278R LEU* 2.6 51.7 + - + +
289R THR* 5.1 2.2 - - - -
291R LEU* 5.1 3.8 - - + -
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Residues in contact with GLU 275 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R ASP* 3.5 6.9 - - - +
32R LYS* 3.0 35.4 + - - +
271R TYR* 2.7 58.8 + - + +
272R THR* 4.0 2.5 - - - +
274R PHE* 1.3 76.4 - - + +
276R ALA* 1.3 65.0 + - - +
278R LEU* 3.5 10.2 - - + +
279R GLU* 2.9 31.1 + - - +
456R LYS* 2.7 42.8 + - + +
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Residues in contact with ALA 276 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102R LEU* 4.8 2.7 - - + -
272R THR 2.9 18.5 + - - +
273R SER 3.8 2.7 - - - +
275R GLU* 1.3 80.1 - - - +
277R MET* 1.3 61.7 + - - +
278R LEU 3.4 0.2 + - - -
279R GLU* 3.6 5.7 + - - +
280R MET* 3.4 23.5 + - - +
456R LYS* 4.0 14.6 - - + +
459R TYR* 3.7 28.5 - - + -
460R SER* 3.7 20.8 - - - +
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Residues in contact with MET 277 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R TYR* 4.0 10.5 + - - +
87R MET* 3.2 43.3 - - + +
88R PHE 4.0 7.9 - - - +
89R LEU* 4.2 7.6 - - + +
102R LEU* 4.8 5.6 - - + +
273R SER 3.0 15.3 + - - +
274R PHE 2.9 4.1 + - - +
276R ALA* 1.3 76.2 - - - +
278R LEU* 1.3 64.5 + - - +
280R MET* 3.3 18.7 - - - +
287R CYS* 3.0 45.5 - - - +
288R ILE* 3.3 8.5 - - - -
289R THR* 3.0 29.2 - - - +
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Residues in contact with LEU 278 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R ALA* 4.9 2.2 - - + -
53R GLU* 3.2 50.3 + - + +
55R SER* 4.9 9.0 - - - +
57R TYR* 4.5 6.3 + - - -
75R LYS* 5.3 6.4 + - - -
274R PHE* 2.6 41.1 + - + +
275R GLU* 3.1 9.6 + - + +
277R MET* 1.3 71.4 - - - +
279R GLU* 1.3 67.8 + - + +
280R MET* 2.9 14.2 + - - +
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Residues in contact with GLU 279 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275R GLU* 2.9 23.9 + - - +
276R ALA* 3.9 6.3 - - - +
278R LEU* 1.3 80.6 - - + +
280R MET* 1.3 58.4 + - - +
281R LYS* 3.6 12.3 + - - +
456R LYS* 3.6 30.9 + - - -
460R SER* 5.6 6.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il